Unit 2: 5

Question 0

Describe protein degradation by ubiquination pathway

Answer 0

In this pathway proteins are targeted for degradation by covalent ligation with ubiquitin, a reaction that requires ATP. Following the binding of the first ubiquitin molecule with the epsilon-amino group of a lysine residue of the substrate protein a polyubiquitin chan is usually formed in which the C terminus of each ubiquitin unit is linked to a specific lysine residue of the previous ubiquitin.

Question 1

Describe the four possible mechanisms of the GroEL-GroES folding machine

Answer 1

1. A true enzyme (that lowers the transition state for folding)
2. “anfinsen box”
3. “Iterative annealing”
   - unfold/misfold protein binds in GroEL cavity and
   - GroES lid binds, deforms cavity, changes interior residues from nonpolar to polar. mechanically unfold protein
   - ATP hydrolysis provides around 13 second timing mechanism
   - GroES dissociates, protein is released to try and refold again
4. Protein can fold faster inside the box than in solution
   - cavity size, charge can affect folding rate
   - same idea as Anfinsen box, but an active, protective container

Question 2

What does the E-1enzyme do?

Answer 2

activates ubiquitin in an ATP driven reaction that creates a high energy covalent, thioester E1-ubiquitin bond

Question 3

What does E2 enzyme do?

Answer 3

transfers activated ubiquitin to the target protein bound to a specific E3 enzyme -again via a thioester E2 ubiquitin intermediate

Question 4

What does E3 enzyme do?

Answer 4

E3 then catalyzes the final transfer to the epsilon amino group of one or more specific lysine residues on the target protein .
This step is usually repeated to generate polyubiquitin chains of various levels.